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Background and Purpose—There is controversy in the literature regarding the relationship between intima-media thickness (IMT) and body composition among adolescents. This study investigated the relationship between body fat percentage and IMT, while controlling for height, weight, age, blood pressure, cholesterol, glucose, triglycerides and VO2max in 12 to 17-year-old children. Methods—111 children (mean age = 14.33 years) participated in this study. Body fat percentage was assessed using dual energy x-ray absorptiometry (DXA). A B-mode, high-resolution ultrasonograph was used to measure the IMT of the right and left common carotid arteries (CCA). Fasting blood tests were performed to obtain blood lipid and glucose profiles. Blood pressure was measured using an automatic blood pressure cuff.Results—Data were divided into body fat tertiles to compare differences between the upper and lower tertile. Contrary to what might be expected, the mean IMT of the group with the lowest body fat percent was 0.516 mm and the mean IMT for the upper tertile of body fat percent was 0.483 mm (F(2,103) = 5.883, p = 0.004). Post hoc analysis indicated that the two leanest groups had significantly thicker IMT than the group with the highest percent body fat (p = 0.005 and p = 0.027, respectively). The two leanest groups were not significantly different from each other. When controlling for gender, no significant relationship existed between CCA-IMT and body fat percentage (F(2,103) = 2.267, p = 0.109). Conclusions—This study found that there were significant differences in IMT between body fat percentage and CCA-IMT in children and adolescents 12 to 17-years of age. This study did indicate that as body fat increases, risk factors such as cholesterol and triglycerides also increase. Overall, the direct relationship between CCA-IMT and body fat percentage is poorly understood in children and adolescents. Further research is necessary to determine a standardized protocol for assessing atherosclerotic risk in adolescents.